[Bioclusters] Need some advice on a cluster for EST/cDNA assembly, clustering

Joe Landman landman at scalableinformatics.com
Mon Feb 28 11:33:40 EST 2005

I might suggest a look at BioBrew or Rocks as a cluster base, as it 
makes the administration aspect fairly simple.

Glen Otero has done a fine job on BioBrew, so most people will not have 
to think hard about the installation.  Support for using BioBrew and 
Rocks is available via email lists, or via companies (Glen's, mine, others).

You could also look at other bits that strive to make the clustering bit 
simple: Warewulf + cAos/Centos/RH/SuSE/..., Oscar (v4 came out a few 
months ago), and others.

There are many options, but simplicity/ease of install and use would be 
along the Rocks/BioBrew direction.  If you need to customize it (many 
labs could run it out of the box), then it gets complex.


Matthew Hudson wrote:
> Another key consideration is: How much sysadmin experience / effort does 
> this life science group have? Maintaining and updating a Linux cluster 
> built from scratch can be a challenge for a group of biology PhDs with 
> no full-time sysadmin, not to mention the cost of power consumtion, 
> cooling etc.. Sun is a little better than building your own Linux 
> system, Apple really try to make this easier and might be a better 
> solution, but their cluster software is expensive. If it's just an EST 
> project you might recommend they get one or two good size SMP machines 
> (maybe the new quad Opterons from Sun, with at least 8GB RAM) and forget 
> about the cluster.

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615

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